Title The Clinical and Genomic Epidemiology of Rhinovirus in Homeless Shelters-King County, Washington.
Author Chow, Eric J; Casto, Amanda M; Roychoudhury, Pavitra; Han, Peter D; Xie, Hong; Pfau, Brian; Nguyen, Tien V; Sereewit, Jaydee; Rogers, Julia H; Cox, Sarah N; Wolf, Caitlin R; Rolfes, Melissa A; Mosites, Emily; Uyeki, Timothy M; Greninger, Alexander L; Hughes, James P; Shim, M Mia; Sugg, Nancy; Duchin, Jeffrey S; Starita, Lea M; Englund, Janet A; Chu, Helen Y
Journal J Infect Dis Publication Year/Month 2022-Oct
PMID 35749582 PMCID PMC9384451
Affiliation + expend 1.Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA.

BACKGROUND: Rhinovirus (RV) is a common cause of respiratory illness in all people, including those experiencing homelessness. RV epidemiology in homeless shelters is unknown. METHODS: We analyzed data from a cross-sectional homeless shelter study in King County, Washington, October 2019-May 2021. Shelter residents or guardians aged >/=3 months reporting acute respiratory illness completed questionnaires and submitted nasal swabs. After 1 April 2020, enrollment expanded to residents and staff regardless of symptoms. Samples were tested by multiplex RT-PCR for respiratory viruses. A subset of RV-positive samples was sequenced. RESULTS: There were 1066 RV-positive samples with RV present every month of the study period. RV was the most common virus before and during the coronavirus disease 2019 (COVID-19) pandemic (43% and 77% of virus-positive samples, respectively). Participants from family shelters had the highest prevalence of RV. Among 131 sequenced samples, 33 RV serotypes were identified with each serotype detected for </=4 months. CONCLUSIONS: RV infections persisted through community mitigation measures and were most prevalent in shelters housing families. Sequencing showed a diversity of circulating RV serotypes, each detected over short periods of time. Community-based surveillance in congregate settings is important to characterize respiratory viral infections during and after the COVID-19 pandemic. CLINICAL TRIALS REGISTRATION: NCT04141917.

StrainID RV Species Serotype Length(nt) Country Year Strain Name
ANC00014 A 85 7124 USA 2017 SC380
ANC00019 A 60 7076 USA 2017 SC42
ANC00024 A 34 7224 USA 2020 A34_7
ANC00029 A 34 7235 USA 2019 A34_2
ANC00034 A 11 7072 USA 2020 A11_3
ANC00039 A 20 6340 USA 2019 A20_1
ANC00044 A 23 7008 USA 2020 A23_3
ANC00049 A 23 7007 USA 2020 A23_8
ANC00054 A 23 7008 USA 2020 A23_13
ANC00059 A 23 7008 USA 2020 A23_18
ANC00064 A 23 7008 USA 2020 A23_23
ANC00069 A 23 7008 USA 2020 A23_28
ANC00074 A 25 7078 USA 2020 A25_2
ANC00079 A 63 6975 USA 2020 A63_1
ANC00084 A 82 7033 USA 2020 A82_1
ANC00089 A 100 7106 USA 2019 A100_2
ANC00094 A 1 7023 USA 2021 RvA1B/USA/2021/YUF486
ANC00099 A 1 7045 USA 2021 RvA1B/USA/2021/WS8YFT
ANC00104 A 1 7045 USA 2021 RvA1B/USA/2021/V9DKA2
ANC00109 A 28 7102 USA 2021 RvA28/USA/2021/T5JCZV
ANC00114 A 20 7121 USA 2021 RvA20/USA/2021/NUHTW4
ANC00119 A 78 7094 USA 2021 RvA78/USA/2021/HZUMHQ
ANC00124 A 23 7008 USA 2021 RvA23/USA/2021/G3QT6A
ANC00129 A 1 7045 USA 2021 RvA1B/USA/2021/CZ5GSB
ANC00134 A 101 7020 USA 2021 RvA101/USA/2021/B67TLB
ANC00139 A 101 7090 USA 2021 RvA101/USA/2021/8WF6RG
ANC00144 A 47 7062 USA 2021 RvA47/USA/2021/6A42AC
ANC00149 A 63 6987 USA 2021 RvA63/USA/2021/XLKES9
ANC00154 A 1 7045 USA 2021 RvA1B/USA/2021/QU9ZFD
ANC00159 A 1 7045 USA 2021 RvA1B/USA/2021/MRGJ7J
ANC00164 A 2 7072 USA 2021 RvA2/USA/2021/GJZVDX
ANC00169 A 1 7032 USA 2021 RvA1B/USA/2021/BGLPMU
ANC00174 A 25 7078 USA 2021 RvA25/USA/2021/8SLLJC
ANC00179 A 1 7040 USA 2021 RvA1B/USA/2021/4U8VMU
ANC00184 A 61 7110 USA 2021 RvA61/USA/2021/2EX6MN
ANC00189 A 60 7022 USA 2021 RvA60/USA/2021/F7HHAW
ANC00194 A 78 7094 USA 2021 RvA78/USA/2021/XYL5Q4
ANC00199 A 49 7056 USA 2021 RvA49/USA/2021/QYDYAG
ANC00204 A 78 7094 USA 2021 RvA78/USA/2021/M46A2K
ANC00209 A 1 7045 USA 2021 RvA1B/USA/2021/9VG3N5
ANM00010 A 101 7124 USA 2017 SC1270
ANM00015 A 21 7023 USA 2017 SC378
ANM00020 A 103 7137 USA 2017 SC16
ANM00025 A 34 7236 USA 2019 A34_6
ANM00030 A 34 7214 USA 2019 A34_1
ANM00035 A 13 7020 USA 2020 A13_1
ANM00040 A 20 6340 USA 2019 A20_2
ANM00045 A 23 7008 USA 2020 A23_4
ANM00050 A 23 7008 USA 2020 A23_9
ANM00055 A 23 7008 USA 2020 A23_14
ANM00060 A 23 7008 USA 2020 A23_19
ANM00065 A 23 7008 USA 2020 A23_24
ANM00070 A 23 7008 USA 2020 A23_29
ANM00075 A 25 7072 USA 2020 A25_3
ANM00080 A 63 6987 USA 2020 A63_2
ANM00085 A 82 7033 USA 2020 A82_2
ANM00090 A 101 7039 USA 2021 A101_1
ANM00095 A 46 7103 USA 2021 RvA46/USA/2021/YU9LWX
ANM00100 A 1 7045 USA 2021 RvA1B/USA/2021/WRH49C
ANM00105 A 101 7039 USA 2021 RvA101/USA/2021/U2NC4T
ANM00110 A 47 7062 USA 2021 RvA47/USA/2021/T4J636
ANM00115 A 1 7045 USA 2021 RvA1B/USA/2021/MZKYMT
ANM00120 A 1 7045 USA 2021 RvA1B/USA/2021/HNEU7L
ANM00125 A 61 7084 USA 2021 RvA61/USA/2021/FUT2YA
ANM00130 A 101 7039 USA 2021 RvA101/USA/2021/CJ9SQ3
ANM00135 A 1 7045 USA 2021 RvA1B/USA/2021/APWHPM
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ANM00145 A 1 7045 USA 2021 RvA1B/USA/2021/3Y86U8
ANM00150 A 30 7058 USA 2021 RvA30/USA/2021/XAC6DR
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ANM00220 A 101 7090 USA 2021 RvA101/USA/2021/UX9Y8D
ANM00225 A 1 7040 USA 2021 RvA1B/USA/2021/RJ9JKH
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ANM00370 A 67 7089 USA 2021 RvA67/USA/2021/JXLCTN
ANM00375 A 1 7045 USA 2021 RvA1B/USA/2021/HBTE45
ANM00380 A 1 7045 USA 2021 RvA1B/USA/2021/EZ2KF3
ANM00385 A 22 7135 USA 2021 RvA22/USA/2021/CCSRHY
ANM00390 A 101 7075 USA 2021 RvA101/USA/2021/AABEL2
ANM00395 A 78 7094 USA 2021 RvA78/USA/2021/7TKCBK
ANM00400 A 78 7094 USA 2021 RvA78/USA/2021/4DAE7N
ANM00405 A 30 7062 USA 2021 RvA30/USA/2021/V62MF8
ANM00410 A 1 7045 USA 2021 RvA1B/USA/2021/RH7JDE
ANM00415 A 11 7073 USA 2021 RvA11/USA/2021/PLXFU8
ANM00420 A 1 6992 USA 2021 RvA1B/USA/2021/MAPNPK
ANM00425 A 1 7045 USA 2021 RvA1B/USA/2021/H23QU5
ANM00430 A 1 7047 USA 2021 RvA1B/USA/2021/CZ5GSB
ANM00435 A 1 7047 USA 2021 RvA1B/USA/2021/97Y7SV
ANM00440 A 31 7124 USA 2021 RvA31/USA/2021/7SD656
ANM00445 A 1 7047 USA 2021 RvA1B/USA/2021/5DSSHD
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ANM00455 A 39 7047 USA 2021 RvA39/USA/2021/UMLKGB
ANM00460 A 1 7047 USA 2021 RvA1B/USA/2021/P4MNWU
ANM00465 A 31 7086 USA 2021 RvA31/USA/2021/LUSRTV
ANM00470 A 1 7045 USA 2021 RvA1B/USA/2021/HMUAKS
ANM00475 A 1 7047 USA 2021 RvA1B/USA/2021/EUEGND
ANM00480 A 60 7004 USA 2021 RvA60/USA/2021/AHYZTF
ANM00485 A 46 7105 USA 2021 RvA46/USA/2021/9QUT2Q
ANM00490 A 1 7047 USA 2021 RvA1B/USA/2021/6JXZSA
ANM00495 A 1 7047 USA 2021 RvA1B/USA/2021/3MB4H3
ANM00500 A 66 7065 USA 2021 RvA66/USA/2021/ZVWUUZ
ANM00505 A 1 7047 USA 2021 RvA1B/USA/2021/TH253U
ANM00510 A 101 7089 USA 2021 RvA101/USA/2021/MXCX3F
ANM00515 A 1 7045 USA 2021 RvA1B/USA/2021/HTGELU
ANM00520 A 101 7075 USA 2021 RvA101/USA/2021/E4FGB8
ANM00525 A 78 7045 USA 2021 RvA78/USA/2021/7VC8Y5
ANM00530 A 78 7141 USA 2021 RvA78/USA/2021/3NPTV7
ANM00535 A 1 7047 USA 2021 RvA1B/USA/2021/MP3DJV
ANM00540 A 1 6966 USA 2021 RvA1B/USA/2021/6MDZV3
ANP00012 A 29 6955 USA 2017 SC815
ANP00017 A 94 7012 USA 2017 SC177
ANP00022 A 34 7238 USA 2020 A34_9
ANP00027 A 34 7232 USA 2019 A34_4
ANP00032 A 11 7069 USA 2020 A11_1
ANP00037 A 13 7020 USA 2020 A13_3
ANP00042 A 23 7008 USA 2020 A23_1
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ANP00052 A 23 7002 USA 2020 A23_11
ANP00057 A 23 7008 USA 2020 A23_16
ANP00062 A 23 7008 USA 2020 A23_21
ANP00067 A 23 7008 USA 2020 A23_26
ANP00072 A 23 7008 USA 2020 A23_31
ANP00077 A 39 7047 USA 2021 A39_1
ANP00082 A 67 7082 USA 2020 A67_2
ANP00087 A 82 7033 USA 2020 A82_4
ANP00092 A 101 7039 USA 2021 A101_3
ANP00097 A 11 7082 USA 2021 RvA11/USA/2021/X97RTD
ANP00102 A 30 7058 USA 2021 RvA30/USA/2021/VWPFHG
ANP00107 A 78 7094 USA 2021 RvA78/USA/2021/THHT34
ANP00112 A 25 7078 USA 2021 RvA25/USA/2021/QLQU2B
ANP00117 A 78 7094 USA 2021 RvA78/USA/2021/MPLXS4
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ANP00127 A 1 7046 USA 2021 RvA1B/USA/2021/DR2R7H
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ANP00137 A 78 7094 USA 2021 RvA78/USA/2021/73UMJP
ANP00142 A 39 7047 USA 2021 RvA39/USA/2021/7FDLJU
ANP00147 A 12 7106 USA 2021 RvA12/USA/2021/2PYKSY
ANP00152 A 1 7045 USA 2021 RvA1B/USA/2021/ST2HNK
ANP00157 A 78 7094 USA 2021 RvA78/USA/2021/MVUA24
ANP00162 A 1 7045 USA 2021 RvA1B/USA/2021/HAUGWA
ANP00167 A 78 7089 USA 2021 RvA78/USA/2021/CVE2ED
ANP00172 A 34 7119 USA 2021 RvA34/USA/2021/9P87Y4
ANP00177 A 78 7094 USA 2021 RvA78/USA/2021/6L9AYA
ANP00182 A 1 7045 USA 2021 RvA1B/USA/2021/3E99XE
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CNM00055 C 33 7073 USA 2021 RvC33/USA/2021/6N55CL
CNM00060 C 13 7059 USA 2021 RvC13/USA/2021/LATCKD
CNP00007 C 56 7041 USA 2017 SC9730
CNP00012 C 17 7069 USA 2020 C17_2
CNP00017 C 13 7045 USA 2021 C13_1
CNP00022 C 15 7031 USA 2021 C15_3
CNP00027 C 20 7086 USA 2021 C20_1
CNP00032 C 29 7049 USA 2020 C29_1
CNP00037 C 36 6995 USA 2021 C36_4
CNP00042 C 48 6951 USA 2020 C48_3
CNP00047 C 7 7039 USA 2021 RvC7/USA/2021/TEZYBU
CNP00052 C 7 7022 USA 2021 RvC7/USA/2021/9YB5N5
CNP00057 C 44 6911 USA 2021 RvC44/USA/2021/SFJ6NZ
CNP00062 C 13 7060 USA 2021 RvC13/USA/2021/CKHXZD
CNS00008 C 34 7060 USA 2017 SC647
CNS00013 C 17 7069 USA 2020 C17_1
CNS00018 C 13 7059 USA 2021 C13_2
CNS00023 C 15 7034 USA 2021 C15_4
CNS00028 C 20 7054 USA 2021 C20_2
CNS00033 C 33 7006 USA 2021 C33_1
CNS00038 C 43 6956 USA 2020 C43_2
CNS00043 C 48 6951 USA 2020 C48_4
CNS00048 C 55 7045 USA 2021 RvC55/USA/2021/P7JDPJ
CNS00053 C 1 6946 USA 2021 RvC1/USA/2021/9HZPGH
CNS00058 C 3 7048 USA 2021 RvC3/USA/2021/PTDPQ7
CNS00063 C 20 7064 USA 2021 RvC20/USA/2021/5AUZVQ
CNS07336 C 19 7076 USA 2020 RvC19/USA/cf466/2020
CNS07337 C 53 7060 USA 2020 RvC26/USA/f25a5/2020
CNZ00011 C 17 7039 USA 2020 C17_3
CNZ00016 C 8 7066 USA 2021 C8_1
CNZ00021 C 15 7034 USA 2020 C15_2
CNZ00026 C 19 7108 USA 2020 C19_1
CNZ00031 C 28 7075 USA 2021 C28_1
CNZ00036 C 36 7013 USA 2021 C36_3
CNZ00041 C 48 6951 USA 2020 C48_2
CNZ00046 C 3 7033 USA 2021 RvC3/USA/2021/U9JKY7
CNZ00051 C 44 7069 USA 2021 RvC44/USA/2021/86PLMK
CNZ00056 C 11 7065 USA 2021 RvC11/USA/2021/2VT7W9
CNZ00061 C 17 7058 USA 2021 RvC17/USA/2021/F439UE
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